Added backwards compatible json parser for custom models and custom modification json files

Author: douweschulte

fuzz/fuzz.rs

@@ -16,7 +16,7 @@ use std::time::Duration;
 
 use std::thread;
 
-#[derive(Parser, Debug)]
+#[derive(Debug, Parser)]
 #[clap(version)]
 struct Args {
     #[clap(help = "Name of the target")]

rustyms/Cargo.toml

@@ -26,6 +26,7 @@ rand = { workspace = true, optional = true }
 rayon = { workspace = true, optional = true }
 regex = { workspace = true }
 serde = { workspace = true }
+serde_json = { workspace = true }
 similar = { workspace = true }
 swash = { workspace = true, optional = true }
 thin-vec = { workspace = true }
@@ -35,7 +36,6 @@ zeno = { workspace = true, optional = true }
 [dev-dependencies]
 base64 = { workspace = true }
 png = { workspace = true }
-serde_json = { workspace = true }
 directories = { workspace = true }
 
 [features]

rustyms/src/annotation/model/built_in.rs

@@ -584,21 +584,3 @@ pub(super) static GLYCAN_LOSSES: LazyLock<Vec<(MonoSaccharide, bool, Vec<Neutral
             ),
         ]
     });
-
-#[test]
-#[expect(clippy::missing_panics_doc)]
-fn test_reading_custom_models_json_2024() {
-    use serde_json;
-    let data = include_str!("custom_model_2024.json");
-    let mods: Vec<(String, FragmentationModel)> = serde_json::from_str(data).unwrap();
-    assert!(mods.len() > 1);
-}
-
-#[test]
-#[expect(clippy::missing_panics_doc)]
-fn test_reading_custom_models_json_2025() {
-    use serde_json;
-    let data = include_str!("custom_model_20250528.json");
-    let mods: Vec<(String, FragmentationModel)> = serde_json::from_str(data).unwrap();
-    assert!(mods.len() > 1);
-}

rustyms/src/annotation/model/custom_models.rs

@@ -0,0 +1,50 @@
+use std::path::Path;
+
+use crate::{
+    error::{Context, CustomError},
+    parse_json::ParseJson,
+    prelude::FragmentationModel,
+};
+
+/// Parse a custom models JSON string. The parser is guaranteed to be backwards compatible
+/// with any JSON made by the serde serialisation of the custom models in previous version of
+/// the library.
+/// # Errors
+/// If the file could not be opened or parsed.
+pub fn parse_custom_models(path: &Path) -> Result<Vec<(String, FragmentationModel)>, CustomError> {
+    let string = std::fs::read_to_string(path).map_err(|err| {
+        CustomError::error(
+            "Could not parse custom models file",
+            err,
+            Context::show(path.display()),
+        )
+    })?;
+    Vec::from_json(&string)
+}
+
+/// Parse a custom models JSON string. The parser is guaranteed to be backwards compatible
+/// with any JSON made by the serde serialisation of the custom models in previous version of
+/// the library.
+/// # Errors
+/// If the string could not be parsed.
+pub fn parse_custom_models_str(
+    value: &str,
+) -> Result<Vec<(String, FragmentationModel)>, CustomError> {
+    Vec::from_json(value)
+}
+
+#[test]
+#[expect(clippy::missing_panics_doc)]
+fn test_reading_custom_models_json_2024() {
+    let data = include_str!("custom_model_2024.json");
+    let mods = parse_custom_models_str(data).unwrap();
+    assert!(mods.len() > 1);
+}
+
+#[test]
+#[expect(clippy::missing_panics_doc)]
+fn test_reading_custom_models_json_2025() {
+    let data = include_str!("custom_model_20250528.json");
+    let mods = parse_custom_models_str(data).unwrap();
+    assert!(mods.len() > 1);
+}

rustyms/src/annotation/model/glycan.rs

@@ -152,9 +152,9 @@ impl GlycanModel {
 #[derive(Clone, Copy, Debug, Deserialize, Eq, Hash, PartialEq, Serialize)]
 pub struct GlycanPeptideFragment {
     /// The full glycan stays attached
-    full: bool,
+    pub(super) full: bool,
     /// The glycan fragments and at any number of monosaccharides within the range (min, max, inclusive) stay attached (any fucoses on these fragments are always included and do not count towards the limit)
-    core: Option<(u8, u8)>,
+    pub(super) core: Option<(u8, u8)>,
 }
 
 impl std::ops::Add<&Self> for GlycanPeptideFragment {